Those are two separate -- not unrelated, but separate -- issues.
First of all, the word enemy has a much broader meaning than someone you want to kill. That's one sense in which the word can be used, but not the only one. I just did a quick Google, and the first definition of "enemy" that came up is "a person who is actively opposed or hostile to someone or something." Ben Shapiro and others like him are obviously enemies of trans people in that respect, because they want to make laws that limit or even eliminate their rights.
Dehumanizing one's enemies is something we should all try to avoid (although it can be VERY hard, especially when they're dehumanizing you), and being able to have a thoughtful conversation with someone you disagree with can be a constructive thing IF the other person is willing to do that (which is not always the csse). Even though I'm just an old, straight, cis, white lady, I can easily see that it can be excruciatingly hard, if not impossible, for a trans person to have such a conversation with someone who literally wants to legislate against their right to exist (and there are plenty of people who want to do so). That's why it's important for cis allies to stand with them and speak up o their behalf, especially at a time like this, when their rights are under fierce attack.
The trans community also needs the rest of us to respect the fact that they know who their enemies are, and that they have the right to call them out. Any oppressed or marginalized group knows damned well who their enemies are, and those who are not a member of such a group do NOT have the right to tell those in the group who their enemies are or are not.
Cis people who want to be allies can do what Neil DeGrasse Tyson did in this video while also being fully aware of who the enemies of the trans community are.